academic/spades: Added (SPAdes Genome Assembler).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

5 files changed, 165 insertions, 0 deletions

diff --git a/academic/spades/README b/academic/spades/README
new file mode 100644
index 0000000000..d28dbb956e
--- /dev/null
+++ b/academic/spades/README
@@ -0,0 +1,16 @@
+SPAdes: a single-cell genome assembler
+
+SPAdes (St. Petersburg genome assembler) is intended for both standard
+isolates and single-cell MDA bacteria assemblies.
+
+SPAdes generates single-cell assemblies, providing information about
+genomes of uncultivatable bacteria that vastly exceeds what may be
+obtained via traditional metagenomics studies.
+
+Citing:
+Nurk S et al. Assembling Single-Cell Genomes and Mini-Metagenomes From
+Chimeric MDA Products. Journal of Computational Biology 20(10) (2013),
+714-737. doi:10.1089/cmb.2013.0084
+
+NOTE!
+This will not build on a 32bit system.
diff --git a/academic/spades/References b/academic/spades/References
new file mode 100644
index 0000000000..7c9e1b455e
--- /dev/null
+++ b/academic/spades/References
@@ -0,0 +1,15 @@
+Related publications
+
+    S. Nurk, A. Bankevich, D. Antipov, A. A. Gurevich, A. Korobeynikov, A. Lapidus, A. D. Prjibelsky, A. Pyshkin, A. Sirotkin, Y. Sirotkin, R. Stepanauskas, J. S. McLean, R. Lasken, S. R. Clingenpeel, T. Woyke, G. Tesler, M. A. Alekseyev, and P. A. Pevzner. Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. Journal of Computational Biology 20(10) (2013), 714-737. doi:10.1089/cmb.2013.0084
+
+    Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021
+
+    Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, and Max A. Alekseyev. Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. Journal of Computational Biology (2012). doi:10.1089/cmb.2012.0098
+
+    Nikolay Vyahhi, Son K. Pham, and Pavel A. Pevzner. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261. doi:10.1007/978-3-642-33122-0_20
+
+    Sergey I. Nikolenko, Anton I. Korobeynikov and Max. A. Alekseyev. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics (2013) 14(S1):S7. doi:10.1186/1471-2164-14-S1-S7
+
+    Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, and Glenn Tesler. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8), pp. 1072-1075. doi:10.1093/bioinformatics/btt086
+
+    Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son Pham, Anton Korobeynikov, Alla Lapidus and Pavel A. Pevzner. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics (2014) 30 (12): i293-i301. doi: 10.1093/bioinformatics/btu266
diff --git a/academic/spades/slack-desc b/academic/spades/slack-desc
new file mode 100644
index 0000000000..dac6b298ce
--- /dev/null
+++ b/academic/spades/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+      |-----handy-ruler------------------------------------------------------|
+spades: spades (SPAdes Genome Assembler)
+spades:
+spades: SPAdes – St. Petersburg genome assembler – is intended for both
+spades: standard isolates and single-cell MDA bacteria assemblies.
+spades:
+spades: Home: http://bioinf.spbau.ru/en/spades
+spades:
+spades:
+spades:
+spades:
+spades:
diff --git a/academic/spades/spades.SlackBuild b/academic/spades/spades.SlackBuild
new file mode 100644
index 0000000000..740b6a1e5f
--- /dev/null
+++ b/academic/spades/spades.SlackBuild
@@ -0,0 +1,105 @@
+#!/bin/sh
+
+# Slackware build script for spades
+
+# Copyright 2015 Petar Petrov petar.petrov@student.oulu.fi
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+PRGNAM=spades
+SRCNAM=SPAdes
+VERSION=${VERSION:-3.5.0}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i486 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i486" ]; then
+  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+set -e
+
+if [ "$ARCH" != "x86_64" ]; then
+  printf "\n\n$ARCH is not supported... \n"
+  exit 1
+fi
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $SRCNAM-$VERSION
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM-$VERSION
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+mkdir -p build
+cd build
+  cmake -G "Unix Makefiles" \
+    -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DLIB_SUFFIX=${LIBDIRSUFFIX} \
+    -DMAN_INSTALL_DIR=/usr/man \
+    -DCMAKE_BUILD_TYPE=Release ../src $*
+  make 
+  make install DESTDIR=$PKG
+cd ..
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  changelog.html README \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/spades/spades.info b/academic/spades/spades.info
new file mode 100644
index 0000000000..2927f5e9ef
--- /dev/null
+++ b/academic/spades/spades.info
@@ -0,0 +1,10 @@
+PRGNAM="spades"
+VERSION="3.5.0"
+HOMEPAGE="http://bioinf.spbau.ru/en/spades"
+DOWNLOAD="UNSUPPORTED"
+MD5SUM=""
+DOWNLOAD_x86_64="http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz"
+MD5SUM_x86_64="58fbf728ec9945b9c36a26ff8c8f4cac"
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="petar.petrov@student.oulu.fi"